I remember in one episode of the anime. Pikachu and Squirtle said that Ekans and Koffing were evil. And Koffing and Ekans replied by saying that they were not evil, only their masters make them do bad things.

So that pretty much says stuffs about how Pokemon react don't they? Also aren't Pokemon like animals? Animals are also vicious sometimes but they're certainly not evil. Also, I don't think Arceus would make an evil Pokemon. What would be the point of making an evil Pokemon?